Personally, I think it is the degree of ho versatile Clefable is. In addition to being one of the hardest to wear down mons in the metagame due to its just good enough bulk in conjunction with Magic Guard and instant healing (though this doesn't hold as true to Unaware clefable due to o hazards and needing wish protect), it just has so many other absolutely valuable options at its disposal. It can run thunder wave to dissuade almost anything (especially spdef talon) aside from Excadrill from coming in, even allowing it to beat some other wise great counters such as venusaur with calm mind added in. It can run Knock Off to remove many mons' passive recovery, especially crippling for heatran, as well as a life orb or another item that would otherwise let clefable be broken. Even deeper in it gets moves such as Stealth Rock, Healing wish, heal bell, wish, etc, all of which are massively important support moves with either limited or restricted distribution .So your argument is literally just that Clefable has Twave. You also argue about "limited movepool" of others, but I mean almost every A+ rank mon has a vast movepool. You also forget like half the shit the example mons have, Landorus-T having access to U-turn, Garchomp having access to Dragon Tail and a massive offensive movepool, and Heatran having Magma Storm, Torment, Taunt, Substitute, and a pretty significant offensive movepool. Being able to heal oneself while being support isn't uncommon either - Latios, Manaphy, Mega Sableye, and Talonflame can all do it.
As far as "BSing by it's checks", that's at least half the shit in A+. The argument that "other pokemon have weaknesses" is pretty dumb, and "uncommon offensive types" isn't true at all-they're mandatory offensive types if you want a ghost of a chance against Mega Altaria. Bisharp, Excadrill, Ferrothorn, Heatran, Magnezone, MMetagross, Scizor, Gengar, Mega Venusaur, Skarmory, and Talonflame can all beat it, so I'm just gonna go ahead and ignore the fact you cherry picked only 3 checks to artificially reinforce your argument. Many of these don't mind being thunder wave'd-and no, you're not getting Fire Blasted if the moveset is Twave/SR/Softboiled/Moonblast.
It's able to wall such a massive portion of the meta, even on both sides of the spectrum simultaneously whilst having issues in being walled itself because of the options clefable has to lure in and cripple its counters, or even outright beat them.
It fits on every playstyle. It requires next to 0 support aside from a heatran or talonflame counter, while giving a ton back. And all of that is without delving into just straight up support and just how many different, yet equally effective spreads it can run.
It is the definition of an S rank Mon.
I'm on mobile so I probably missed a few things here or there, so feel free to chime in on this. (Also almost all of those things you said don't mind being parad hate it)
Edit: also clefable counters aren't hard counters really due to some tricks it can pull, whereas things like mega scizor or garchomp definitely have very exploitable weaknesses.